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You aren't missing anything. That is how the kindle and calibre work together.
Amazon provides no way for calibre to update metadata for books (or anything else, for that matter), so automatic management doesn't do much on a Kindle (calibre keeps its own metadata cache up to date). This is also why collection information is not updated on kindles. You end up with two copies because the path names have metadata in them. You can delete the old copy before or after sending the new one.
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